6-138218163-T-C
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_021635.3(PBOV1):āc.233A>Gā(p.His78Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000384 in 1,613,860 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. H78L) has been classified as Uncertain significance.
Frequency
Consequence
NM_021635.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PBOV1 | NM_021635.3 | c.233A>G | p.His78Arg | missense_variant | 1/1 | ENST00000527246.3 | |
ARFGEF3 | NM_020340.5 | c.351+8122T>C | intron_variant | ENST00000251691.5 | |||
ARFGEF3 | XR_001743524.2 | n.499+8122T>C | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PBOV1 | ENST00000527246.3 | c.233A>G | p.His78Arg | missense_variant | 1/1 | NM_021635.3 | P1 | ||
ARFGEF3 | ENST00000251691.5 | c.351+8122T>C | intron_variant | 1 | NM_020340.5 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000723 AC: 11AN: 152240Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000598 AC: 15AN: 251006Hom.: 0 AF XY: 0.0000516 AC XY: 7AN XY: 135642
GnomAD4 exome AF: 0.0000349 AC: 51AN: 1461620Hom.: 0 Cov.: 31 AF XY: 0.0000316 AC XY: 23AN XY: 727090
GnomAD4 genome AF: 0.0000723 AC: 11AN: 152240Hom.: 0 Cov.: 32 AF XY: 0.0000672 AC XY: 5AN XY: 74380
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Feb 28, 2023 | The c.233A>G (p.H78R) alteration is located in exon 1 (coding exon 1) of the PBOV1 gene. This alteration results from a A to G substitution at nucleotide position 233, causing the histidine (H) at amino acid position 78 to be replaced by an arginine (R). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at